DOCSLIB.ORG

Mouse Paxip1 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Paxip1 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Paxip1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Paxip1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Paxip1 gene (NCBI Reference Sequence: NM_018878 ; Ensembl: ENSMUSG00000002221 ) is located on Mouse chromosome 5. 21 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 21 (Transcript: ENSMUST00000002291). Exon 4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Paxip1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-25H24 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous mutant mice are developmentally retarded and embyronic lethal by E9.5. Exon 4 starts from about 8.24% of the coding region. The knockout of Exon 4 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 2244 bp, and the size of intron 4 for 3'-loxP site insertion: 5742 bp. The size of effective cKO region: ~564 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 4 21 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Paxip1 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(7064bp) | A(24.89% 1758) | C(19.78% 1397) | T(30.97% 2188) | G(24.36% 1721) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr5 - 27781736 27784735 3000 browser details YourSeq 97 279 459 3000 87.1% chr12 + 55445497 55445688 192 browser details YourSeq 90 328 535 3000 81.8% chr2 + 156692659 156692845 187 browser details YourSeq 85 303 459 3000 88.9% chr8 + 36178905 36179078 174 browser details YourSeq 80 277 459 3000 87.1% chr3 - 97644200 97834641 190442 browser details YourSeq 77 293 459 3000 88.9% chr6 + 35264936 35265109 174 browser details YourSeq 76 272 374 3000 92.4% chr5 + 141222729 141222851 123 browser details YourSeq 74 335 458 3000 89.4% chr2 - 3272560 3272694 135 browser details YourSeq 74 277 459 3000 88.6% chr17 - 28465794 28465993 200 browser details YourSeq 72 321 682 3000 95.1% chr4 - 54912010 54912547 538 browser details YourSeq 71 330 572 3000 92.8% chr2 + 146548266 146548727 462 browser details YourSeq 71 279 464 3000 82.3% chr1 + 153545980 153546155 176 browser details YourSeq 70 320 423 3000 85.9% chr10 + 18324061 18324177 117 browser details YourSeq 69 303 423 3000 87.1% chr7 + 101045374 101045510 137 browser details YourSeq 67 321 404 3000 91.5% chr3 - 152295787 152295883 97 browser details YourSeq 67 337 463 3000 93.6% chr2 + 166778951 166779088 138 browser details YourSeq 66 294 404 3000 84.3% chr2 - 73709881 73709990 110 browser details YourSeq 66 293 374 3000 92.7% chr9 + 121743150 121843908 100759 browser details YourSeq 65 115 458 3000 71.7% chrX + 94131098 94131251 154 browser details YourSeq 64 321 484 3000 93.3% chr9 - 57856993 57857506 514 Note: The 3000 bp section upstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr5 - 27778172 27781171 3000 browser details YourSeq 131 2519 2870 3000 82.0% chr12 - 25347169 25347642 474 browser details YourSeq 123 2510 2851 3000 89.8% chr8 - 106427949 106428300 352 browser details YourSeq 102 2511 2806 3000 91.9% chr9 + 32318193 32318571 379 browser details YourSeq 96 2509 2725 3000 76.4% chr7 - 99376600 99376815 216 browser details YourSeq 95 2588 2806 3000 90.0% chr14 - 66888430 66888723 294 browser details YourSeq 89 2528 2806 3000 93.4% chr13 + 74170492 74170785 294 browser details YourSeq 84 2510 2724 3000 85.6% chr9 - 62568482 62568769 288 browser details YourSeq 84 2589 2806 3000 89.8% chr15 + 7841264 7841479 216 browser details YourSeq 80 2584 2724 3000 85.5% chr5 + 101626128 101626266 139 browser details YourSeq 79 2514 2763 3000 86.8% chr5 + 128658419 128658702 284 browser details YourSeq 79 2575 2744 3000 90.7% chr12 + 17009229 17009425 197 browser details YourSeq 78 2537 2724 3000 87.4% chr2 - 129266227 129266416 190 browser details YourSeq 78 2509 2740 3000 78.6% chr14 - 33242183 33242421 239 browser details YourSeq 78 2519 2805 3000 84.4% chr11 + 55280398 55280682 285 browser details YourSeq 77 2537 2724 3000 87.3% chr11 - 4011068 4011260 193 browser details YourSeq 75 2520 2724 3000 87.8% chr7 - 138053041 138053259 219 browser details YourSeq 75 2511 2733 3000 77.0% chr2 + 139768128 139768330 203 browser details YourSeq 74 2513 2744 3000 85.8% chr3 - 40898591 40898819 229 browser details YourSeq 73 2509 2717 3000 85.3% chr14 - 58681745 58681951 207 Note: The 3000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found. Page 4 of 8 https://www.alphaknockout.com Gene and protein information: Paxip1 PAX interacting (with transcription-activation domain) protein 1 [ Mus musculus (house mouse) ] Gene ID: 55982, updated on 12-Aug-2019 Gene summary Official Symbol Paxip1 provided by MGI Official Full Name PAX interacting (with transcription-activation domain) protein 1 provided by MGI Primary source MGI:MGI:1890430 See related Ensembl:ENSMUSG00000002221 Gene type protein coding RefSeq status REVIEWED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as PTIP; D5Ertd149e Summary This gene encodes a nuclear-localized protein that contains six BRCT1 (C-terminal of breast cancer susceptibility protein) Expression domains. The encoded protein is involved in the repair of DNA double-strand breaks and is necessary for progression through cell division. The protein also functions in the regulation of transcription by recruiting histone methyltransferases to gene promoters bound by the sequence-specific transcription factor paired box protein 2 (Pax2). [provided by RefSeq, Mar 2013] Orthologs Ubiquitous expression in thymus adult (RPKM 12.1), ovary adult (RPKM 11.4) and 28 other tissues See more human all Genomic context Location: 5 B1; 5 13.23 cM See Paxip1 in Genome Data Viewer Exon count: 22 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (27740080..27791672, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (28067205..28117879, complement) Chromosome 5 - NC_000071.6 Page 5 of 8 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Paxip1 ENSMUSG00000002221 Description PAX interacting (with transcription-activation domain) protein 1 [Source:MGI Symbol;Acc:MGI:1890430] Gene Synonyms D5Ertd149e, PTIP Location Chromosome 5: 27,740,080-27,791,691 reverse strand. GRCm38:CM000998.2 About this gene This gene has 7 transcripts (splice variants), 203 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 34 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Paxip1- ENSMUST00000002291.11 5850 1056aa ENSMUSP00000002291.7 Protein coding CCDS39039 Q6NZQ4 TSL:1 201 GENCODE basic APPRIS P1 Paxip1- ENSMUST00000196734.1 749 92aa ENSMUSP00000142578.1 Nonsense mediated - A0A0G2JE02 TSL:3 204 decay Paxip1- ENSMUST00000199714.1 3829 No - Retained intron - - TSL:NA 206 protein Paxip1- ENSMUST00000197625.1 736 No - Retained intron - - TSL:2 205 protein Paxip1- ENSMUST00000196641.1 717 No - Retained intron - - TSL:2 203 protein Paxip1- ENSMUST00000196605.1 515 No - Retained intron - - TSL:2 202 protein Paxip1- ENSMUST00000199993.4 381 No - lncRNA - - TSL:3 207 protein Page 6 of 8 https://www.alphaknockout.com 71.61 kb Forward strand 27.74Mb 27.76Mb 27.78Mb 27.80Mb Contigs < AC146612.2 Genes (Comprehensive set... < Paxip1-201protein coding < Paxip1-205retained intron < Paxip1-203retained intron < Paxip1-204nonsense mediated decay < Paxip1-207lncRNA < Paxip1-202retained intron < Paxip1-206retained intron Regulatory Build 27.74Mb 27.76Mb 27.78Mb 27.80Mb Reverse strand 71.61 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding merged Ensembl/Havana Non-Protein
Load more

Recommended publications
  • DOWNREGULATION of PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH Huijuan Song
    The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 8-2011 DOWNREGULATION OF PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH huijuan song Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biology Commons, Cancer Biology Commons, Cell Biology Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation song, huijuan, "DOWNREGULATION OF PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH" (2011). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 165. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/165 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. DOWNREGULATION OF PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH by Huijuan Song, MD, MS APPROVED: -------------_.-._.__.._-----------­ APPROVED: Dean, The University of Texas, Health Science Center at Houston Graduate School of Biomedical Sciences DOWNREGULATION OF PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH A DISSERTATION Presented to the Faculty of The University of Texas Health Science Center at Houston and The University of Texas M.
    [Show full text]
  • CPTC-TP53BP1-1 (CAB079980) Immunohistochemistry Immunofluorescence
    CPTC-TP53BP1-1 (CAB079980) Uniprot ID: Q12888 Protein name: TP53B_HUMAN Full name: TP53-binding protein 1 Function: Double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis (PubMed:12364621, PubMed:22553214, PubMed:23333306, PubMed:17190600, PubMed:21144835, PubMed:28241136). Plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage by promoting non-homologous end joining (NHEJ)- mediated repair of DSBs and specifically counteracting the function of the homologous recombination (HR) repair protein BRCA1 (PubMed:22553214, PubMed:23727112, PubMed:23333306). In response to DSBs, phosphorylation by ATM promotes interaction with RIF1 and dissociation from NUDT16L1/TIRR, leading to recruitment to DSBs sites (PubMed:28241136). Recruited to DSBs sites by recognizing and binding histone H2A monoubiquitinated at 'Lys-15' (H2AK15Ub) and histone H4 dimethylated at 'Lys-20' (H4K20me2), two histone marks that are present at DSBs sites (PubMed:23760478, PubMed:28241136, PubMed:17190600). Required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (PubMed:23345425). Participates in the repair and the orientation of the broken DNA ends during CSR (By similarity). In contrast, it is not required for classic NHEJ and V(D)J recombination (By similarity). Promotes NHEJ of dysfunctional telomeres via interaction with PAXIP1 (PubMed:23727112). Subcellular
    [Show full text]
  • MLL3 Suppresses Tumorigenesis Through Regulating TNS3 Enhancer Activity
    Zheng et al. Cell Death and Disease (2021) 12:364 https://doi.org/10.1038/s41419-021-03647-2 Cell Death & Disease ARTICLE Open Access MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity Jun-Yi Zheng1,2, Chen-Yu Wang1,2,ChuanGao1,2,QiongXiao1,2,Cheng-WeiHuang1,2,MinWu 1,2 and Lian-Yun Li1,2 Abstract MLL3 is a histone H3K4 methyltransferase that is frequently mutated in cancer, but the underlying molecular mechanisms remain elusive. Here, we found that MLL3 depletion by CRISPR/sgRNA significantly enhanced cell migration, but did not elevate the proliferation rate of cancer cells. Through RNA-Seq and ChIP-Seq approaches, we identified TNS3 as the potential target gene for MLL3. MLL3 depletion caused downregulation of H3K4me1 and H3K27ac on an enhancer ~ 7 kb ahead of TNS3. 3C assay indicated the identified enhancer interacts with TNS3 promoter and repression of enhancer activity by dCas9-KRAB system impaired TNS3 expression. Exogenous expression of TNS3 in MLL3 deficient cells completely blocked the enhanced cell migration phenotype. Taken together, our study revealed a novel mechanism for MLL3 in suppressing cancer, which may provide novel targets for diagnosis or drug development. Introduction lower expression than the average proximal genes, indi- Enhancers are cis-acting elements for transcription cating H3K27ac as an active enhancer hallmark10. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; factor binding and activate transcription over a long dis- H3K27ac enriched regions in the intergenic chromatin are tance. One of the important features for enhancers is that now used to identify active enhancers3,11,12. Generally, specific patterns of histone modifications occupy the H3K4me3 marks the gene transcription start sites (TSS)13.
    [Show full text]
  • Open Data for Differential Network Analysis in Glioma
    International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes.
    [Show full text]
  • EBF1 Drives Hallmark B Cell Gene Expression by Enabling the Interaction of PAX5 with the MLL H3K4 Methyltransferase Complex Charles E
    www.nature.com/scientificreports OPEN EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex Charles E. Bullerwell1, Philippe Pierre Robichaud1,2, Pierre M. L. Deprez1, Andrew P. Joy1, Gabriel Wajnberg1, Darwin D’Souza1,3, Simi Chacko1, Sébastien Fournier1, Nicolas Crapoulet1, David A. Barnett1,2, Stephen M. Lewis1,2 & Rodney J. Ouellette1,2* PAX5 and EBF1 work synergistically to regulate genes that are involved in B lymphocyte diferentiation. We used the KIS-1 difuse large B cell lymphoma cell line, which is reported to have elevated levels of PAX5 expression, to investigate the mechanism of EBF1- and PAX5-regulated gene expression. We demonstrate the lack of expression of hallmark B cell genes, including CD19, CD79b, and EBF1, in the KIS-1 cell line. Upon restoration of EBF1 expression we observed activation of CD19, CD79b and other genes with critical roles in B cell diferentiation. Mass spectrometry analyses of proteins co-immunoprecipitated with PAX5 in KIS-1 identifed components of the MLL H3K4 methylation complex, which drives histone modifcations associated with transcription activation. Immunoblotting showed a stronger association of this complex with PAX5 in the presence of EBF1. Silencing of KMT2A, the catalytic component of MLL, repressed the ability of exogenous EBF1 to activate transcription of both CD19 and CD79b in KIS-1 cells. We also fnd association of PAX5 with the MLL complex and decreased CD19 expression following silencing of KMT2A in other human B cell lines. These data support an important role for the MLL complex in PAX5-mediated transcription regulation.
    [Show full text]
  • Comparative Transcriptomics Reveals Similarities and Differences
    Seifert et al. BMC Cancer (2015) 15:952 DOI 10.1186/s12885-015-1939-9 RESEARCH ARTICLE Open Access Comparative transcriptomics reveals similarities and differences between astrocytoma grades Michael Seifert1,2,5*, Martin Garbe1, Betty Friedrich1,3, Michel Mittelbronn4 and Barbara Klink5,6,7 Abstract Background: Astrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic and epigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades. Methods: We utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry. Results: Our analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth.
    [Show full text]
  • Identification of Microdeletion of 7Q36.1-Qter in Fetal Hemivertebrae with Scoliosis
    ISSN: 2574-1241 Volume 5- Issue 4: 2018 DOI: 10.26717/BJSTR.2018.09.001876 Xiaofang Sun. Biomed J Sci & Tech Res Research Article Open Access Identification of Microdeletion of 7q36.1-qter in Fetal Hemivertebrae with Scoliosis Yingjun Xie1, Wei Jian2, Jingsi Chen2, Dunjin Chen2 and Xiaofang Sun*1 1Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, China 2Prenatal Diagnosis Department, The Third Affiliated Hospital of Guangzhou Medical University, China Received: : October 01, 2018; Published: : October 11, 2018 *Corresponding author: Xiaofang Sun, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Duobao Road 63#, 510150, Guangzhou, China Abstract disability. Here we describe a case of fetus with hemivertebrae and scoliosis and detected a 6.42 Mb pure microdeletion at 7q36.1-qter by The 7q36 microdeletion has been identified in patients with variant phenotypes including sacral agenesis, holoprosencephaly and intellectual chromosomal microarray analysis (CMA) that was not determined by traditional karyotyping. This microdeletion was confirmed by Fluorescent describedin situ hybridization an important (FISH) relationship assay. Accurate between breakpoints fetal hemivertebrae of the deletion with scoliosis in this case and 7q36.1-qterwere used to microdeletion establish correlations overlap with between
    [Show full text]
  • UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent Permalink https://escholarship.org/uc/item/7m04f0b0 Author Buchholz, Kyle Stephen Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Kyle Stephen Buchholz Committee in Charge: Professor Jeffrey Omens, Chair Professor Andrew McCulloch, Co-Chair Professor Ju Chen Professor Karen Christman Professor Robert Ross Professor Alexander Zambon 2016 Copyright Kyle Stephen Buchholz, 2016 All rights reserved Signature Page The Dissertation of Kyle Stephen Buchholz is approved and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2016 iii Dedication To my beautiful wife, Rhia. iv Table of Contents Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents ................................................................................................................ v List of Figures ...................................................................................................................
    [Show full text]
  • Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair
    Article Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair Guillaume Brysbaert *, Jérôme de Ruyck, Marc Aumercier and Marc F. Lensink * University of Lille, CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, F-59000 Lille, France; [email protected] (J.R.); [email protected] (M.A.) * Correspondence: [email protected] (G.B.); [email protected] (M.F.L.); Tel.: +33-(0)3-2043-4883 Received: 31 January 2019; Accepted: 5 March 2019; Published: 8 March 2019 Abstract: The transcription factor Ets-1 (ETS proto-oncogene 1) shows low expression levels except in specific biological processes like haematopoiesis or angiogenesis. Elevated levels of expression are observed in tumor progression, resulting in Ets-1 being named an oncoprotein. It has recently been shown that Ets-1 interacts with two DNA repair enzymes, PARP-1 (poly(ADP-ribose) polymerase 1) and DNA-PK (DNA-dependent protein kinase), through two different domains and that these interactions play a role in cancer. Considering that Ets-1 can bind to distinctly different domains of two DNA repair enzymes, we hypothesized that the interaction can be transposed onto homologs of the respective domains. We have searched for sequence and structure homologs of the interacting ETS(Ets-1), BRCT(PARP-1) and SAP(DNA-PK) domains, and have identified several candidate binding pairs that are currently not annotated as such. Many of the Ets-1 partners are associated to DNA repair mechanisms. We have applied protein-protein docking to establish putative interaction poses and investigated these using centrality analyses at the protein residue level.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • An Ensemble of the Icluster Method to Analyze Longitudinal Lncrna Expression Data for Psoriasis Patients
    University of Kentucky UKnowledge Internal Medicine Faculty Publications Internal Medicine 4-20-2021 An Ensemble of the iCluster Method to Analyze Longitudinal lncRNA Expression Data for Psoriasis Patients Suyan Tian The First Hospital of Jilin University, China Chi Wang University of Kentucky, [email protected] Follow this and additional works at: https://uknowledge.uky.edu/internalmedicine_facpub Part of the Biostatistics Commons, Genomics Commons, Internal Medicine Commons, and the Oncology Commons Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Repository Citation Tian, Suyan and Wang, Chi, "An Ensemble of the iCluster Method to Analyze Longitudinal lncRNA Expression Data for Psoriasis Patients" (2021). Internal Medicine Faculty Publications. 239. https://uknowledge.uky.edu/internalmedicine_facpub/239 This Article is brought to you for free and open access by the Internal Medicine at UKnowledge. It has been accepted for inclusion in Internal Medicine Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. An Ensemble of the iCluster Method to Analyze Longitudinal lncRNA Expression Data for Psoriasis Patients Digital Object Identifier (DOI) https://doi.org/10.1186/s40246-021-00323-6 Notes/Citation Information Published in Human Genomics, v. 15, issue 1, article no. 23. © The Author(s). 2021 This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
    [Show full text]
  • Knockdown of Long Non-Coding RNA LOC100132707 Inhibits the Migration of Uveal Melanoma Cells Via Silencing JAK2
    OncoTargets and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH Knockdown of Long Non-Coding RNA LOC100132707 Inhibits the Migration of Uveal Melanoma Cells via Silencing JAK2 This article was published in the following Dove Press journal: OncoTargets and Therapy Ying Qi Background/Objective: Although lots of long non-coding RNAs (lncRNAs) have been Renjie Yao demonstrated to be involved in carcinogenesis, the functions of numerous of lncRNAs Wenjing Zhang remain unknown. Bioinformatics online database showed that lncRNA LOC100132707 Qingqing Cui was highly expressed in metastatic melanoma tissues, and its expression predicted a lower Fengyan Zhang overall survival rate in melanoma patients. However, LOC100132707 function in uveal melanoma (UM) progression still remains unclear. In the present study, we aimed to Department of Ophthalmology, The First elucidate the role and molecular mechanisms underlying LOC100132707 in UM. AffiliatedHospital of Zhengzhou University, The Laboratory for Ophthalmology and Methods: RT-PCR was used to detect the levels of LOC100132707 in UM cells. Cell Vision Science, Henan Eye Hospital, migration, invasion and tumorigenesis were tested by using the transwell chamber assay and Zhengzhou 450052, Henan, People’s in vivo assay. Republic of China Results: LOC100132707 expression in metastatic UM cell line MM28 was significantly higher than that of the non-metastatic UM cell lines, MP38, MP46 and MP65, as well as the expressions of LOC100132707-related genes, including XRN1, PARP14, JAK2, DDX60, BUB1 and SAMD9L. LOC100132707 downregulation significantly repressed cell migration and invasion abilities, whereas overexpressing JAK2 rescued these effects. Consistently, upregulation of LOC100132707 induced significant increases in cell migration and invasion abilities via upregulating JAK2.
    [Show full text]